[FieldTrip] possible bugs in using mask in ft_topoplotTFR?

Clara A. Scholl clara.scholl at gmail.com
Tue Dec 18 21:04:27 CET 2012


Dear Berry,

I found that the mask works when plotting  topos directly from an
average field (grandavg.avg), but not when plotting the individual
data ( grandavg.individual -- which are averaged from the individual
field, so effectively the same thing).  Can you try averaging over the
first dimension of grandavg.individual
(grandavg.avg=squeeze(mean(grandavg.individual))) and removing the
individual field? Does that work?

Good luck,
Clara

On Tue, Dec 18, 2012 at 2:56 PM, berry van den berg
<berryv.dberg at gmail.com> wrote:
> Hi Fieldtrip experts,
>
> Im working on an EEG analysis in fieldtrip and I came across some possible
> bugs or perhaps I am doing something wrong.... I have a dataset with 28
> subjects and my grandavg (including the 28 individuals) look like this:
>
> grandavg =
>
>     individual: [28x64x1251 double]
>          label: {64x1 cell}
>           time: [1x1251 double]
>         dimord: 'subj_chan_time'
>            cfg: [1x1 struct]
>           mask: [1x64 double]
>
>  I first tried to use a mask in ft_topoplotER in the  11/11/2012 fieldtrip
> version but this did not work:
>
> input:
>
> cfg = [];
> cfg.xlim = [0.3 0.4];
> cfg.baseline = [-.2 0];
> cfg.layout = ft_prepare_layout(timelock_mat{1,1})
> cfg.interactive='yes';
> grandavg.mask = [ones(1, 60) zeros(1,4)]; %just an example
> cfg.maskparameter = 'mask';
> ft_topoplotER(cfg,grandavg)
>
> Reference to non-existent field 'mask'.
> Error in ft_topoplotTFR (line 713)
>   datmask = data.(cfg.maskparameter);
>
> it seems that around line 420 in the function   data =
> ft_timelockanalysis(tmpcfg, data) it does not retrieve the mask parameter.
>
> To check if it was an old bug I downloaded the newest FT version:
> 16/12/2012: the mask parameter does not work in this version yet..
>
> Moreover:
> topoplotTFR line 409-411 there is a section added compared to version
> 11/11/2012:
>
> %%%%%%%
> if isfield(cfg, 'parameter') && ~isfield(data, cfg.parameter)
>   error('cfg.parameter=%s is not present in data structure', cfg.parameter);
> end
> %%%%%%%
>
> which checks whether the is present... but because I have all my individual
> subjects in the data I am waiting for line 425:data =
> ft_timelockanalysis(tmpcfg, data) to average my dataset. It crashes here
> (after removal of these lines it runs like normal)
>
> Error using ft_topoplotTFR (line 412)
> cfg.parameter=avg is not present in data structure
>
> Is there something I am missing?
>
> Thanks a lot! (also for providing this very good package!)
>
> Berry
>
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